I've run into a problem in EoF and was hoping someone could give some guidance on how to correct this.  I tabbed a song in Guitar Pro, imported it to EoF, and when I save it and run it through rstk some of the chord fingerings have changed so that it's physically impossible to play it.  Any idea how to keep it fingerings the same?

Generally EOF imports the fingerings as defined in the GP file, but if a chord has no defined fingering EOF will come up with some on its own.

 

One quick way to look for fingering differences is to enable the Bandfuse color set (File>Preferences>Preferences) and then the note coloring will reflect which finger each note is fretted with: Open string = purple, index = green, middle = red, ring = yellow, pinky = blue, thumb = orange. If a note's fingering isn't defined, EOF will guess based on any fret hand position in effect, otherwise if no suitable fingering is determined, the note is drawn in white. If the note uses tap technique, it is drawn in black.

 

At the very least, it should mostly reflect how it would end up in-game with what is manually defined and what EOF uses for undefined fingerings.

 

If you want to define fingerings for chords that are missing that information, you can use "Song>Rocksmith>Correct chord fingerings"